---------- Forwarded message ----------
From: <wmsmith.uci.edu>
Date: Mon, May 21, 2012 at 5:45 PM
Subject: Re: Fwd: [AMBER] Amber tools 12 and esp visualization in VMD and
PyMol
To: "Ray Luo, Ph.D." <ray.luo.uci.edu>
Cc: Wesley Smith <wmsmith.uci.edu>, Sudarshan Debnath <
sudarshandebnath.ku.rediffmail.com>, Ray Luo <ray.luo.uci.edu>
Dr. Sudarshan Debnath,
It looks like you are displaying the raw potential isosurface under the
"points" drawing method. This usually doens't come out very good. If you
are after the zero-potential isosurface, using the "Solid Surface"
option under the "Draw" pulldown menu will give you much a much better
looking surface. If you want to project the potential to the molecular
surface you will need to load the molecule from the .top and .rst first
and then load the phi.dx file into it.
Section 8.4.2 through 8.4.12 in the AmberTools12 manual
(
http://ambermd.org/doc12/AmberTools12.pdf) explain how to use the
potential and levelset dx files for visualization in VMD.
If you forward me the phi.dx file I will see if I can get it working as a
surface map for the van der waals molecular surface (using the radii in
the .top file).
-Wes
> Okay, let's first work on VMD first since it's an asci file ...
>
> I'm forwarding your files to Wes who implemented the VMD visualization
> option ...
>
> All the best,
> Ray
>
> ---------- Forwarded message ----------
> From: Sudarshan Debnath <sudarshandebnath.ku.rediffmail.com>
> Date: Mon, May 21, 2012 at 12:11 PM
> Subject: [AMBER] Amber tools 12 and esp visualization in VMD and PyMol
> To: amber.ambermd.org
>
>
> Dear Ray and Qin,
>
> I install Amber tools 12 as you suggested and calculate the electrostatic
> potential. I am very sorry to say the same problem is arises that is the
> pbsa.phi is not loaded in PyMol (PyMol stop working). In the VMD the
> pbsa_phi.dx is loaded but the isosurface representation is not acceptable
> (please see the image attached with mail). I also analyze again the two
> mdout file (created by Qin and me). Now there is no remarkable difference,
> the two mdout file is same. So something is different in pbsa.phi and
> pbsa_phi.dx file. I attached pbsa_phi.dx file in next mail. Please check
> it. Why this problem arises, is there any thing that I miss? Please let me
> know. I told that I successfully loaded the pbsa.phi in PyMol using Amber
> Tools 1.5, but it is a wrong result, because the esp gradient can not be
> appeared by this result. I am very sorry for that.
>
> With best regards,
> Sudarshan.
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>
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Received on Mon May 21 2012 - 18:00:03 PDT
